This page keeps the long module map out of the README while preserving a single place to look up entrypoints.
THESIS WORKFLOW PHASE THESIS SKILLS MODULE
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1. Reference library
· EndNote export 00-bib-endnote/
· Zotero sync 00-bib-zotero/
2. Draft migration and review handoff
· Word → LaTeX 01-word-to-latex/
· LaTeX → review-friendly Word 02-latex-to-word/
· Review diff and TODOs 03-latex-review-diff/
· Word feedback ingest 04-word-review-ingest/
3. Check phase
· Reference integrity 10-check-references/
· Final reference set 17-final-reference-set/
· Language baseline checks 11-check-language/
· Format structure checks 12-check-format/
· Content completeness checks 13-check-content/
· Deep language screening 14-check-language-deep/
· Compile diagnostics 15-check-compile/
4. Fix phase
· Reference fixes 20-fix-references/
· Language style fixes 21-fix-language-style/
· Format structure fixes 22-fix-format-structure/
· Deep language patches 24-fix-language-deep/
5. Submission readiness
· PASS / WARN / BLOCK gate 16-check-readiness/
6. External verification (alpha)
· CrossRef / OpenAlex lookup 18-verify-references/
6.5 Hallucination risk (v3.0)
· Deterministic risk scoring 19-check-hallucination-risk/
6.6 Claim-citation support triage (v3.1)
· Deterministic triage scoring 20-check-claim-citation/
6.7 Final-audit foundations
· Process residue scanning 23-check-final-cleanup/
· Statistical notation consistency 25-check-statistical-consistency/
· Manual contents anchor checks 26-check-manual-anchor/
· JSON handoff aggregation 27-final-audit-report/
· Reference audit ledger 28-reference-audit-ledger/
· Static HTML report index 29-report-index/
· Final audit HTML detail 30-final-audit-html/
· Reference ledger HTML detail 31-reference-ledger-html/
· Claim-citation HTML detail 32-claim-citation-html/
7. Defense preparation
· Outline, figure inventory, notes 17-defense-pack/
8. Institutional adaptation
· Custom rule packs 90-rules/
| Stage | Module | Entrypoint | Output / role |
|---|---|---|---|
| Bibliography | 00-bib-zotero/ |
sync_from_word.py |
Extract Zotero citations from Word and create stable mapping artifacts |
| Bibliography | 00-bib-zotero/ |
check_bib_quality.py |
Check BibTeX quality: missing fields, DOI shape, language metadata |
| Bibliography | 00-bib-endnote/ |
check_endnote_export.py |
Preflight exported EndNote XML/RIS/BibTeX files |
| Bibliography | 00-bib-endnote/ |
import_library.py |
Normalize EndNote exports into stable refNNN IDs |
| Migration | 01-word-to-latex/ |
migrate_project.py |
Map Word-exported content into a LaTeX project structure |
| Migration | 02-latex-to-word/ |
migrate_project.py |
Generate review-friendly .docx and report degraded elements |
| Review | 03-latex-review-diff/ |
review_diff.py |
Generate review diff, triage, and TODO artifacts |
| Review | 04-word-review-ingest/ |
feedback_ingest.py |
Normalize Word feedback into structured issues |
| Check | 10-check-references/ |
check_references.py |
Validate local citation integrity: cited keys, BibTeX fields, duplicate keys, and local log citation warnings |
| Check | 11-check-language/ |
check_language.py |
Run deterministic language checks, including CJK/Latin spacing |
| Check | 12-check-format/ |
check_format.py |
Check figure/table blocks, labels, references, and front matter |
| Check | 13-check-content/ |
check_content.py |
Check abstract metadata and content structure |
| Check | 14-check-language-deep/ |
check_language_deep.py |
Flag higher-order language and consistency review items |
| Check | 15-check-compile/ |
check_compile.py |
Parse existing LaTeX compile logs into structured diagnostics |
| Gate | 16-check-readiness/ |
check_readiness.py |
Aggregate reports into PASS / WARN / BLOCK readiness artifact |
| Check | 17-final-reference-set/ |
build_final_reference_set.py |
Parse .aux / .bbl or TeX fallback and write final-reference-set-report.json plus final-reference-set-report.csv |
| Verify (alpha) | 18-verify-references/ |
verify_external_references.py |
Query CrossRef / OpenAlex / Semantic Scholar for selected bibliography entries; write external-verification-report.json, missing-doi-candidates.json, and url-verification-report.json |
| Risk (v3.0) | 19-check-hallucination-risk/ |
check_hallucination_risk.py |
Score bibliography entries for hallucination risk; write hallucination-risk-report.json and high-risk-references.csv |
| Triage (v3.1+) | 20-check-claim-citation/ |
check_claim_citation.py |
Extract citation contexts and triage claim-citation pairs by structural support, local metadata-overlap, grouped-cluster, and citation-needed advisory signals; write claim-citation-triage-report.json, claim-citation-triage.md, and claim-citation-triage.csv with support-review enrichment fields |
| Final audit | 23-check-final-cleanup/ |
check_final_cleanup.py |
Scan final LaTeX source for process residue such as TODO, FIXME, ???, blue text markers, draft, and debug; write final-cleanup-report.json without modifying source files |
| Final audit | 25-check-statistical-consistency/ |
check_statistical_consistency.py |
Report mixed statistical notation families such as p值/P值, p=/P=, confidence interval notation, Bootstrap terms, and SMD terms; write statistical-consistency-report.json without rewriting source files |
| Final audit | 26-check-manual-anchor/ |
check_manual_anchor.py |
Report manual \addcontentsline entries that may lack a nearby preceding \phantomsection; write manual-anchor-report.json without repairing anchors or numbering |
| Final audit | 27-final-audit-report/ |
build_final_audit_report.py |
Aggregate existing final-audit, readiness, citation, and reference evidence into final-audit-report.json without rerunning checks or rewriting source files |
| Final audit | 28-reference-audit-ledger/ |
build_reference_audit_ledger.py |
Aggregate existing reference evidence into reference-audit-ledger.csv with one spreadsheet-friendly row per source-specific reference status |
| Report UX | 29-report-index/ |
build_report_index.py |
Generate static local reports/index.html linking JSON / CSV source-of-truth artifacts without replacing them |
| Report UX | 30-final-audit-html/ |
build_final_audit_html.py |
Generate static local reports/final-audit-report.html from final-audit-report.json with verdict, KPI, dimension matrix, issues, and source links |
| Report UX | 31-reference-ledger-html/ |
build_reference_audit_ledger_html.py |
Generate static local reports/reference-audit-ledger.html from reference-audit-ledger.csv with summary stats, scope views, key-grouped slices, and full-table browsing |
| Report UX | 32-claim-citation-html/ |
build_claim_citation_html.py |
Generate static local reports/claim-citation-triage.html from claim-citation-triage-report.json with P0 / P1 / P2 / P3 review groups, issue-card summaries, citation-needed candidates, uncited references, cluster review, and deep links to readiness / references / claim-citation / final-audit while preserving JSON / CSV source artifacts |
| Defense | 17-defense-pack/ |
generate_outline.py |
Generate thesis outline for defense preparation |
| Defense | 17-defense-pack/ |
generate_figure_inventory.py |
Inventory figures and visual evidence |
| Defense | 17-defense-pack/ |
generate_talk_prep_notes.py |
Generate editable talk-prep notes |
| Fix | 20-fix-references/ |
fix_references.py |
Preview and apply reference-related patches |
| Fix | 21-fix-language-style/ |
fix_language_style.py |
Preview and apply deterministic language style patches |
| Fix | 22-fix-format-structure/ |
fix_format_structure.py |
Preview and apply format-structure patches |
| Fix | 23-fix-final-cleanup/ |
fix_final_cleanup.py |
Preview and apply safe final cleanup marker removals |
| Fix | 25-fix-statistical-consistency/ |
fix_statistical_consistency.py |
Preview and apply safe statistical notation normalization |
| Fix | 26-fix-manual-anchor/ |
fix_manual_anchor.py |
Preview and apply safe manual anchor insertion |
| Fix | 28-fix-reference-audit-ledger/ |
fix_reference_audit_ledger.py |
Preview and apply safe removal of truly unused bibliography entries |
| Fix | 24-fix-language-deep/ |
fix_language_deep.py |
Preview deeper language patch candidates |
| Rules | 90-rules/ |
create_pack.py |
Create institution- or journal-specific rule packs |
| Rules | 90-rules/ |
lint_pack.py |
Validate rule-pack structure and write scorecard summaries |
| Rules | 90-rules/ |
export_pack.py |
Export linted rule-pack handoff bundles |
| Runner | repository root | run_check_once.py |
Run the deterministic check pipeline once |
| Runner | repository root | run_evidence_pipeline.py |
Orchestrate final reference set plus all citation evidence layers in sequence |
| Workflow | 33-final-delivery/ |
run_final_delivery.py |
Run final delivery workflow: evidence, checks, optional fixes, bundle rebuild |
| Runner | repository root | run_fix_cycle.py |
Preview or apply report-driven fix cycles; modes: safe, suggest, mixed, final-audit, all |
- Start with
run_check_once.pyif you only want to know the current state of a project. - Start with
00-bib-zotero/or00-bib-endnote/if citation metadata is unstable. - Start with
02-latex-to-word/when the advisor review format is Word but the source of truth is LaTeX. - Start with
16-check-readiness/after reports exist and you need a one-page handoff verdict. - Start with
19-check-hallucination-risk/when you want a fast screen for AI-drafted or suspicious references. - Start with
23-check-final-cleanup/before final PDF/submission handoff when you want to catch process residue without auto-editing the thesis. - Start with
25-check-statistical-consistency/when you need final-stage statistical notation consistency evidence. - Start with
26-check-manual-anchor/when manual TOC / LOF / LOT entries may affect PDF hyperlink jump targets. - Start with
27-final-audit-report/after source-of-truth JSON reports exist and you need a single final-audit handoff artifact. - Start with
28-reference-audit-ledger/when you need a spreadsheet handoff across local citation integrity, final reference set, external verification, DOI, URL, and hallucination-risk evidence. - Start with
29-report-index/when you want a local static HTML landing page for generated JSON / CSV artifacts. - Start with
30-final-audit-html/when you want a readable local detail page for the aggregated final-audit JSON. - Start with
31-reference-ledger-html/when you want a readable local HTML surface for the aggregated reference-audit CSV ledger. - Start with
32-claim-citation-html/when you want a readable local HTML surface for claim-citation support review groups, issue-card summaries, and citation-needed candidates without changing JSON / CSV source artifacts.